Introduction:
Blogo is a web-based tool that detects and displays statistically significant position-specific sequence bias with reduced background noise. The over-represented and under-represented symbols in a particular position are shown above and below the zero line. When the sequences are in open reading frames, the background frequency of nucleotides could be calculated separately for the three positions of a codon, thus greatly reducing the background noise. The χ2 test or fisher's exact test is used to evaluate the statistical significance of every symbol in every position and only those that are significant are highlighted in the resulting logo.

You can run Blogo here. Some examples of sequences logo created by Blogo are here. For help. click here.

Blogo source code:
The perl source code of the program is free under the GNU Lesser General Public License. You can build your own website using the code or run Blogo locally to do some batch analysis.